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update constraint writing
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update constraint writing


Former-commit-id: 5d37cbd
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@enio23
enio23 committed Apr 21, 2020
1 parent 649aa99 commit 51a63d9
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2 changes: 1 addition & 1 deletion DESCRIPTION
100644 → 100755
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@@ -1,6 +1,6 @@
Package: CARNIVAL
Title: A CAusal Reasoning tool for Network Identification (from gene expression data) using Integer VALue programming
Version: 0.99.42
Version: 0.99.43
Author: Enio Gjerga <[email protected]>
Panuwat Trairatphisan
Anika Liu
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47 changes: 29 additions & 18 deletions R/write_binaries.R
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Expand Up @@ -4,25 +4,36 @@

write_binaries <- function(variables=variables){

binaries <- c()
# binaries <- c()
#
# for(i in seq_len(length(variables))){
#
# binaries <- c(binaries,
# paste0("\t",
# variables[[i]]$variables[variables[[i]]$idxNodesUp]))
# binaries <- c(binaries,
# paste0("\t",
# variables[[i]]$variables[variables[[i]]$idxNodesDown]))
# binaries <- c(binaries,
# paste0("\t",
# variables[[i]]$variables[variables[[i]]$idxEdgesUp]))
# binaries <- c(binaries,
# paste0("\t",
# variables[[i]]$variables[variables[[i]]$idxEdgesDown]))
#
# }

for(i in seq_len(length(variables))){

binaries <- c(binaries,
paste0("\t",
variables[[i]]$variables[variables[[i]]$idxNodesUp]))
binaries <- c(binaries,
paste0("\t",
variables[[i]]$variables[variables[[i]]$idxNodesDown]))
binaries <- c(binaries,
paste0("\t",
variables[[i]]$variables[variables[[i]]$idxEdgesUp]))
binaries <- c(binaries,
paste0("\t",
variables[[i]]$variables[variables[[i]]$idxEdgesDown]))

}
i = 1

return(binaries)
cc1 <- paste0("\t",
variables[[i]]$variables[variables[[i]]$idxNodesUp])
cc2 <- paste0("\t",
variables[[i]]$variables[variables[[i]]$idxNodesDown])
cc3 <- paste0("\t",
variables[[i]]$variables[variables[[i]]$idxEdgesUp])
cc4 <- paste0("\t",
variables[[i]]$variables[variables[[i]]$idxEdgesDown])

return(c(cc1, cc2, cc3, cc4))

}
39 changes: 0 additions & 39 deletions R/write_binaries_all_conditions.R
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131 changes: 83 additions & 48 deletions R/write_boundaries.R
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Expand Up @@ -4,57 +4,92 @@

write_boundaries <- function(variables=variables, oF=oF){

## M <- 100
##
## bounds <- c()
##
## for(i in seq_len(length(variables))){
##
## bounds <- c(bounds,
## paste0("\t",
## "-1 <= ",
## variables[[i]]$variables[variables[[i]]$idxNodes],
## " <= 1"))
## bounds <- c(bounds,
## paste0("\t",
## "0 <= ",
## variables[[i]]$variables[variables[[i]]$idxNodesUp],
## " <= 1"))
## bounds <- c(bounds,
## paste0("\t",
## "0 <= ",
## variables[[i]]$variables[variables[[i]]$idxNodesDown],
## " <= 1"))
## bounds <- c(bounds,
## paste0("\t",
## "0 <= ",
## variables[[i]]$variables[variables[[i]]$idxEdgesUp],
## " <= 1"))
## bounds <- c(bounds,
## paste0("\t",
## "0 <= ",
## variables[[i]]$variables[variables[[i]]$idxEdgesDown],
## " <= 1"))
## bounds <- c(bounds, paste0("\t",
## "-1 <= ",
## variables[[i]]$variables[variables[[i]]$idxB],
## " <= 1"))
## bounds <- c(bounds, paste0("\t",
## "0 <= ",
## variables[[i]]$variables[variables[[i]]$idxDist],
## " <= ", M))
## bounds <- c(bounds, paste0("\t",
## "0 <= ",
## unique(strsplit(oF, split = " ")[[1]][grep(
## pattern = "absDiff",
## x = strsplit(oF, split = " ")[[1]])]),
## " <= 2"))
## bounds <- c(bounds, paste0("\t", "0 <= ",
## variables[[i]]$variables[variables[[i]]$idxDist],
## " <= ", M))
##
## }

M <- 100

bounds <- c()
i = 1

for(i in seq_len(length(variables))){

bounds <- c(bounds,
paste0("\t",
"-1 <= ",
variables[[i]]$variables[variables[[i]]$idxNodes],
" <= 1"))
bounds <- c(bounds,
paste0("\t",
"0 <= ",
variables[[i]]$variables[variables[[i]]$idxNodesUp],
" <= 1"))
bounds <- c(bounds,
paste0("\t",
"0 <= ",
variables[[i]]$variables[variables[[i]]$idxNodesDown],
" <= 1"))
bounds <- c(bounds,
paste0("\t",
"0 <= ",
variables[[i]]$variables[variables[[i]]$idxEdgesUp],
" <= 1"))
bounds <- c(bounds,
paste0("\t",
"0 <= ",
variables[[i]]$variables[variables[[i]]$idxEdgesDown],
" <= 1"))
bounds <- c(bounds, paste0("\t",
"-1 <= ",
variables[[i]]$variables[variables[[i]]$idxB],
" <= 1"))
bounds <- c(bounds, paste0("\t",
"0 <= ",
variables[[i]]$variables[variables[[i]]$idxDist],
" <= ", M))
bounds <- c(bounds, paste0("\t",
"0 <= ",
unique(strsplit(oF, split = " ")[[1]][grep(
pattern = "absDiff",
x = strsplit(oF, split = " ")[[1]])]),
" <= 2"))
bounds <- c(bounds, paste0("\t", "0 <= ",
variables[[i]]$variables[variables[[i]]$idxDist],
" <= ", M))

}
cc1 <- paste0("\t",
"-1 <= ",
variables[[i]]$variables[variables[[i]]$idxNodes],
" <= 1")
cc2 <- paste0("\t",
"0 <= ",
variables[[i]]$variables[variables[[i]]$idxNodesUp],
" <= 1")
cc3 <- paste0("\t",
"0 <= ",
variables[[i]]$variables[variables[[i]]$idxNodesDown],
" <= 1")
cc4 <- paste0("\t",
"0 <= ",
variables[[i]]$variables[variables[[i]]$idxEdgesUp],
" <= 1")
cc5 <- paste0("\t",
"0 <= ",
variables[[i]]$variables[variables[[i]]$idxEdgesDown],
" <= 1")
cc6 <- paste0("\t", "-1 <= ", variables[[i]]$variables[variables[[i]]$idxB],
" <= 1")
cc7 <- paste0("\t", "0 <= ", variables[[i]]$variables[variables[[i]]$idxDist],
" <= ", M)
cc8 <- paste0("\t", "0 <= ", unique(strsplit(oF, split = " ")[[1]][grep(
pattern = "absDiff",
x = strsplit(oF, split = " ")[[1]])]),
" <= 2")
cc9 <- paste0("\t", "0 <= ", variables[[i]]$variables[variables[[i]]$idxDist],
" <= ", M)

return(bounds)
return(c(cc1, cc2, cc3, cc4, cc5, cc6, cc7, cc8, cc9))

}
82 changes: 0 additions & 82 deletions R/write_boundaries_all_conditions.R
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26 changes: 16 additions & 10 deletions R/write_constraints_1_all.R
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Expand Up @@ -5,16 +5,22 @@

write_constraints_1_all <- function(variables=variables){

constraints1 <- c()

for(i in seq_len(length(variables))){

var <- variables[[i]]

constraints1 <- c(constraints1, write_constraints_1(variables = var,
conditionIDX = i))

}
## constraints1 <- c()
##
## for(i in seq_len(length(variables))){
##
## var <- variables[[i]]
##
## constraints1 <- c(constraints1, write_constraints_1(variables = var,
## conditionIDX = i))
##
## }

i = 1

var <- variables[[i]]

constraints1 <- write_constraints_1(variables = var, conditionIDX = i)

return(constraints1)

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26 changes: 16 additions & 10 deletions R/write_constraints_2_all.R
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Expand Up @@ -5,16 +5,22 @@

write_constraints_2_all <- function(variables=variables){

constraints2 <- c()

for(i in seq_len(length(variables))){

var <- variables[[i]]

constraints2 <- c(constraints2, write_constraints_2(variables = var,
conditionIDX = i))

}
## constraints2 <- c()
##
## for(i in seq_len(length(variables))){
##
## var <- variables[[i]]
##
## constraints2 <- c(constraints2, write_constraints_2(variables = var,
## conditionIDX = i))
##
## }

i= 1

var <- variables[[i]]

constraints2 <- write_constraints_2(variables = var, conditionIDX = i)

return(constraints2)

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